Abstract
BackgroundHazels (Corylus spp.) are economically important nut-producing species in which ovule development determines seed plumpness, one of the key parameters reflecting nut quality. microRNAs (miRNAs) play important roles in RNA silencing and the post-transcriptional regulation of gene expression. However, very little is currently known regarding the miRNAs involved in regulating ovule growth and development.ResultsIn this study, we accordingly sought to determine the important miRNAs involved in ovule development and growth in hazel. We examined ovules at four developmental stages, namely, ovule formation (Ov1), early ovule growth (Ov2), rapid ovule growth (Ov3), and ovule maturity (Ov4). On the basis of small RNA and mRNA sequencing using the Illumina sequencing platform, we identified 970 miRNAs in hazel, of which 766 and 204 were known and novel miRNAs, respectively. In Ov1-vs-Ov2, Ov1-vs-Ov3, Ov1-vs-Ov4, Ov2-vs-Ov3, Ov2-vs-Ov4, and Ov3-vs-Ov4 paired comparisons, 471 differentially expressed microRNAs (DEmiRNAs) and their 3117 target differentially expressed messenger RNAs (DEmRNAs) formed 11,199 DEmiRNA/DEmRNA pairs, with each DEmiRNA changing the expression of an average of 6.62 target mRNAs. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of all DEmRNAs revealed 29 significantly enriched KEGG pathways in the six paired comparisons, including protein export (ko03060), fatty acid elongation (ko00062), starch and sucrose metabolism (ko00500), fatty acid biosynthesis (ko00061), and amino sugar and nucleotide sugar metabolism (ko00520). Our results indicate that DEmiRNA/DEmRNA pairs showing opposite change trends were related to stress tolerance, embryo and seed development, cell proliferation, auxin transduction, and the biosynthesis of proteins, starch, and fats may participate in ovule growth and development.ConclusionsThese findings contribute to a better understanding of ovule development at the level of post-transcriptional regulation, and lay the foundation for further functional analyses of hazelnut ovule growth and development.
Highlights
Hazels (Corylus spp.) are economically important nut-producing species in which ovule development determines seed plumpness, one of the key parameters reflecting nut quality. microRNAs play important roles in RNA silencing and the post-transcriptional regulation of gene expression
We focused on reads with length between 18 and 30 nt, and these reads were mapped to public databases [Silva, GtRNAdb, Rfam, and Repbase] (Table 2) to annotate the composition of the small RNA populations
We identified a total of 970 miRNAs in hazel, 471 of which were found to be differentially expressed in six paired stage-wise comparisons
Summary
Hazels (Corylus spp.) are economically important nut-producing species in which ovule development determines seed plumpness, one of the key parameters reflecting nut quality. microRNAs (miRNAs) play important roles in RNA silencing and the post-transcriptional regulation of gene expression. Hazels (Corylus spp.) are economically important nut-producing species in which ovule development determines seed plumpness, one of the key parameters reflecting nut quality. Our previous comparative transcriptome analysis showed that genes related to auxin biosynthesis, transport, signaling, the floral quartet model, and flower development may regulate ovary formation and fertilization in hazel [4, 5]. There are initially two ovules in the ovary of hazel, and both of these ovules are fertilized, generally only one will develop into an edible kernel [6]. Ovule size gradually increases from fertilization to maturity, the detailed molecular mechanisms underlying the regulation of ovule growth during the course of development have yet to be fully elucidated
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